Matrix metalloproteinases (MMPs), as the enzymes to degrade extracellular matrix proteins, play a major role on cell behaviors. Among them, MMP-9 usually catalyzes the degradation of proteins with the dominant cleavage at G/L site. Recent high-throughput screening suggests that S/L is a new major site for the cleavage when the substrates of MMP-9 are oligopeptides. Here we examine the cleavage sites of the N-terminal substituted short oligopeptides as the substrates of MMP-9. As the first example of such study of N-substituted small peptides, our results suggest that the substitute group at the N-terminal and the length of peptides significantly affect the position of the cleavage site on the oligopeptides, which provides a useful insight for the design of small peptide derivatives as the substrates of MMP-9. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 790–795, 2013.
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